The metro tunnels are currently facing challenges associated with thermal pollution, which significantly affects their operational safety and energy consumption. The subway source heat pump system (SSHPS) with front-end tunnel lining capillary heat exchangers (CHEs) is an effective technology to address this problem. The heat transfer characteristics of SSHPS have been previously investigated; however, there is a lack of research on the thermal performance of tunnel lining CHEs under groundwater seepage. This study established a numerical simulation model of tunnel lining CHEs based on a demonstration project of SSHPS. Subsequently, the influence of groundwater seepage on the heat transfer characteristics of tunnel lining CHEs was comprehensively analyzed. The findings suggest that an increase in groundwater seepage velocity leads to the initial expansion and subsequent contraction of the thermal influence range caused by CHEs. Simultaneously, the performance of CHEs is enhanced with increasing flow velocity. When the seepage velocity increases from 0 to 1 × 10−4 m/s, the heat exchange capacity per meter and efficiency of the CHEs during the cooling season increase by 450 % and 446 %, respectively. During the heating season, they experience a growth of 320 % and 310 %, respectively. In addition, the heat exchange performance of CHEs is also influenced by the relative flow direction between the fluid within CHEs and the groundwater. The counter flow arrangement exhibits a 7.7 % higher efficiency of heat exchange during the cooling season compared to the parallel flow arrangement, and a 3.9 % higher efficiency of heat exchange during the heating season. Therefore, it is highly recommended to evaluate groundwater seepage conditions during the design phase of SSHPS in order to enhance the performance of tunnel lining CHEs. This study serves as a valuable theoretical reference for the design of tunnel lining CHEs.